I wonder if I can make the directory of input pdb file in jupyter notebook in BioBB MD protein-ligand setup and create a single topology using -merge all option of gromacs. I need your suggestions, please.
we talked in a private e-mail conversation about the possibility to use a PDB file from your own computer in the Jupyter Notebook demonstration tutorials. About the merge option for the pdb2gmx, it is not yet integrated in the current biobb version (v3.0), but we are using it in the development version. An issue has been added to the biobb_md GitHub repo so that we don’t forget to add it in the new version.